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Mol Cell. 2019 Jul 25;75(2):252-266.e8. doi: 10.1016/j.molcel.2019.04.030. Epub 2019 Jun 12.

Topoisomerase II-Induced Chromosome Breakage and Translocation Is Determined by Chromosome Architecture and Transcriptional Activity.

Author information

1
Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD, USA; The Hakubi Center for Advanced Research and Radiation Biology Center, Graduate School of Biostudies, Kyoto University, Kyoto, Japan.
2
Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD, USA.
3
Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, NIH, Bethesda, MD, USA.
4
Research Institute of Molecular Pathology, Vienna Biocenter, Vienna, Austria.
5
Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton BN1 9RQ, UK.
6
Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton BN1 9RQ, UK; Department of Genome Dynamics, Institute of Molecular Genetics of the Czech Academy of Sciences, 142 20 Prague, 4, Czech Republic.
7
Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD, USA. Electronic address: andre_nussenzweig@nih.gov.

Abstract

Topoisomerase II (TOP2) relieves torsional stress by forming transient cleavage complex intermediates (TOP2ccs) that contain TOP2-linked DNA breaks (DSBs). While TOP2ccs are normally reversible, they can be "trapped" by chemotherapeutic drugs such as etoposide and subsequently converted into irreversible TOP2-linked DSBs. Here, we have quantified etoposide-induced trapping of TOP2ccs, their conversion into irreversible TOP2-linked DSBs, and their processing during DNA repair genome-wide, as a function of time. We find that while TOP2 chromatin localization and trapping is independent of transcription, it requires pre-existing binding of cohesin to DNA. In contrast, the conversion of trapped TOP2ccs to irreversible DSBs during DNA repair is accelerated 2-fold at transcribed loci relative to non-transcribed loci. This conversion is dependent on proteasomal degradation and TDP2 phosphodiesterase activity. Quantitative modeling shows that only two features of pre-existing chromatin structure-namely, cohesin binding and transcriptional activity-can be used to predict the kinetics of TOP2-induced DSBs.

KEYWORDS:

3D chromatin organization; DNA double-strand breaks; TDP2; chromosomal translocations; cohesin; proteasome; quantitative modeling; topoisomerase; topoisomerase 2 cleavage complex; transcription

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